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Bioinformatics Advance Access originally published online on October 11, 2006
Bioinformatics 2006 22(23):2918-2925; doi:10.1093/bioinformatics/btl497
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Cell++—simulating biochemical pathways

Chris Sanford 1,2,{dagger}, Matthew L.K. Yip 1,{dagger}, Carl White 1,2 and John Parkinson 1,2,3,*

1 Hospital for Sick Children, 555 University Avenue Toronto, ON, M5G 1X8, Canada
2 Department of Molecular and Medical Genetics, University of Toronto Toronto, ON, Canada
3 Department of Biochemistry, University of Toronto ON, Canada

*To whom correspondence should be addressed.

Motivation: With the generation of a wealth of information, detailing cellular components, their functions and interactions, there is a growing need for the development of new computational tools capable of interpreting these data within spatial and dynamic contexts. Here, we introduce Cell++, a novel stochastic simulation environment with the capacity to study a wide variety of biochemical processes within a spatial context.

Results: Focusing on three case studies, we highlight the potential impact of spatial organization in the evolution and engineering of signaling and metabolic pathways. In addition to altering signaling and metabolic efficiency, simulations also demonstrated features consistent with the phenomenon of metabolic channeling.

Availability: Cell++ is licensed under the GNU general public license (GPL) and has been successfully implemented under Linux and IRIX operating systems. Source code together with a simple tutorial is available at http://www.compsysbio.org/CellSim/.

Contact: jparkin{at}sickkids.ca

Supplementary information: Supplementary data for this paper are available at Bioinformatics online.

Received on June 1, 2006; revised on September 21, 2006; accepted on September 27, 2006

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